This plugin enables you to mutate any residue of a PDB structure
into one of the non-natural L- or D-sidechains of the SwissSidechain
If you do not have PyMOL, it can be obtained here
You should also have Python 2.7+ installed on your machine.
Automatic installation from a terminal (Mac + Linux):
- Download and unzip the file PySwissSidechain.zip in a
directory of your choice.
- Go to the new PySwissSidechain directory and run the
installation script (# ./install.sh).
You will be asked to give the path to your PyMOL application.
On Mac, if PyMOL is in the Applications folder, this should be
something like: "/Applications/MacPyMOL.app/".
give the path of the directory containing the pymol/ folder. This is
typically the directory where you have untarred the
Manual installation (Mac + Linux + Windows):
- Copy all files from the fragments directory into
- Create a directory
- Copy the two files from the SwissSidechains directory in this
- Copy mutagenesis1.py into
- Copy PySwissSidechain.py into
Note that on Windows, the PYMOL_PATH would typically look like
"C:\Program Files\PyMOL" and pymol is sometimes spelled PyMOL
depending on the version of PyMOL you are using.
Plugin Menu (on Mac,version 1.0 to 1.4)
Go under the Plugin->PySwissSidechain:
- Enter the residue you want to mutate as: Object//Chain/ResNumber/
- Enter the new residue code (e.g., HLEU)
Use the command:
Mutate Object//Chain/ResNumber/, Newres
For instance, to mutate residue number '82' on chain 'E' in object
'complex' into Homoleucine (HLEU), write:
Mutate complex//E/82/, HLEU
You can then choose between the different rotamers by clicking on
the arrows at the lower right corner (same as standard Mutagenesis).
Click 'Apply' and 'Done' to validate your mutation.
If you only have one object, you can simply write:
Mutate Chain/ResNumber/, Newres
For MacPyMOL1.5+, you need to explicitly load the plug everytime you
or you can rename MacPyMOL applications to MacPyMOLX11Hybrid.
Use the Pymol plugin D_PySwissSidechain.zip.
Instal it in the same way as the PySwissSidechain plugin.
The plugin appears under Plugin->D_PySwissSidechain.
line uses 'D_Mutate' instead of 'Mutate'.
Older versions of MacPyMOL (0.99)
For older versions of PyMOL (such as 0.99), download these two files
You also need to manually load the plugin by running the command:
everytime you open MacPyMOL.